Identification of proteins in human substantia nigra

Abstract

Characterization of the human brain proteome is a critical area of research. While examination of the human cortex has provided some insight, very little is known about the proteome of the human midbrain, which demonstrates substantial loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) in Parkinson's disease (PD). Therefore, characterization of this region is essential to a better understanding of the pathogenesis of PD. This dataset paper reports two separate studies, where human SNpc was collected from PD and control subjects and 1263 proteins were identified using MALDI-TOF/TOF as well as linear ion trap MS platforms. With gene ontology analysis, the proteins were categorized according to their biological processes, as well as cellular components. These data were also compared with previous proteomic characterization of the human frontal and temporal cortex, and cerebrospinal fluid to establish shared proteins of relevance. The present dataset is the most extensive survey of the human SNpc proteome, to date. Further characterization of the SNpc proteome will significantly facilitate our understanding of the function and expression of proteins involved in PD, as well as provide potential proteins that may be utilized as biomarkers.

Proteomic profiling of the substantia nigra demonstrates CNDP2 overexpression in Parkinson's disease

“…So far, only a small number of proteomic studies exploring the SN of PD patients has been published, four to the best of our knowledge [10][11][12][13]. This probably reflects the difficulty to obtain human tissues, although this type of sample represents, in our view, a source of choice to detect PD specific abnormalities [26].…”

“…A limited number of proteomic studies investigating human post-mortem SN has been published so far in the field of PD research [10][11][12][13]. In the absence of fully satisfying PD animal models, human autopsy tissues represent a unique opportunity to highlight PD specific abnormalities.…”

Cerebrospinal Fluid Peptides as Potential Parkinson Disease Biomarkers: A Staged Pipeline for Discovery and Validation*

“…Proteomics Data Mining for PD-related Proteins/Peptides-Proteomic data were gathered from our previous quantitative PD-related proteomic studies, including a general human CSF profiling (19), two general human midbrain profiling studies (20,21), general human frontal cortex profiling studies of PD progression (22)(23)(24), glycoprotein profiling studies of human CSF and frontal cortex (25), a phosphoprotein profiling of human frontal cortex (unpublished data), glyco-and phospho-protein profiling studies in a MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) monkey model (putamen; unpublished data). A total of 15 data sets were integrated: two on the human CSF proteome, four on the human midbrain (substantia nigra) proteome, six on the human frontal cortex proteome, and the remaining three on the monkey putamen proteome.…”

Enrichment of single neurons and defined brain regions from human brain tissue samples for subsequent proteome analysis

“…Therefore, the molecular analysis of single neuronal cell populations is expected to yield a better understanding of disease mechanisms. Although several groups in the past few years have used proteomics and other molecular biology techniques to study the brain and the mechanisms underlying neurodegenerative diseases, many questions still remain unanswered (Dumont et al 2006;Kitsou et al 2008;Werner et al 2008;He et al 2006). Changes in specific neuronal populations are commonly masked in global analyses, where whole brains or large sections rather than specific cell groups are homogenized for analysis.…”